pgmio.cpp

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/*
 * Author: Steven Ludtke, 04/10/2003 (sludtke@bcm.edu)
 * Copyright (c) 2000-2006 Baylor College of Medicine
 *
 * This software is issued under a joint BSD/GNU license. You may use the
 * source code in this file under either license. However, note that the
 * complete EMAN2 and SPARX software packages have some GPL dependencies,
 * so you are responsible for compliance with the licenses of these packages
 * if you opt to use BSD licensing. The warranty disclaimer below holds
 * in either instance.
 *
 * This complete copyright notice must be included in any revised version of the
 * source code. Additional authorship citations may be added, but existing
 * author citations must be preserved.
 *
 * This program is free software; you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation; either version 2 of the License, or
 * (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 *
 * */
 
#include "pgmio.h"
#include "geometry.h"
#include "util.h"
#include "portable_fileio.h"
 
using namespace EMAN;
 
const char *PgmIO::MAGIC_BINARY = "P5";
const char *PgmIO::MAGIC_ASCII = "P2";
 
PgmIO::PgmIO(const string & fname, IOMode rw)
:       ImageIO(fname, rw), is_big_endian(true),
        nx(0), ny(0), maxval(0), minval(0),
        file_offset(0), rendermin(0), rendermax(0), renderbits(16)
{}
 
PgmIO::~PgmIO()
{
        if (file) {
                fclose(file);
                file = 0;
        }
}
 
//anonymous namespace make this function local for this file
namespace
{
        int read_int_and_space(FILE * in)
        {
                char buf[32];
                int c = 0;
 
                int i = 0;
                while (!isspace(c = getc(in))) {
                        buf[i] = static_cast < char >(c);
                        i++;
                }
 
                return atoi(buf);
        }
}
 
void PgmIO::init()
{
        ENTERFUNC;
 
        if (initialized) {
                return;
        }
 
        initialized = true;
 
        bool is_new_file = false;
        file = sfopen(filename, rw_mode, &is_new_file, true);
 
        if (!is_new_file) {
                const int bufsz = 1024;
                char buf[bufsz];
 
                buf[0] = static_cast < char >(getc(file));
                buf[1] = static_cast < char >(getc(file));
                buf[2] = '\0';
                getc(file);
 
                if (!is_valid(&buf)) {
                        throw ImageReadException(filename, "invalid PGM file");
                }
 
                char c = '\0';
 
                while ((c = static_cast < char >(getc(file))) == '#') {
                        fgets(buf, bufsz, file);
                }
                ungetc(c, file);
 
                nx = read_int_and_space(file);
                ny = read_int_and_space(file);
                maxval = read_int_and_space(file);
 
                if (nx <= 0 || ny <= 0) {
                        throw ImageReadException(filename, "file size < 0");
                }
 
                file_offset = portable_ftell(file);
        }
        EXITFUNC;
}
 
bool PgmIO::is_valid(const void *first_block)
{
        ENTERFUNC;
        bool result = false;
        if (first_block) {
                result = Util::check_file_by_magic(first_block, MAGIC_BINARY);
        }
        EXITFUNC;
        return result;
}
 
int PgmIO::read_header(Dict & dict, int image_index, const Region * area, bool)
{
        ENTERFUNC;
 
        //single image format, index can only be zero
        if(image_index == -1) {
                image_index = 0;
        }
 
        if(image_index != 0) {
                throw ImageReadException(filename, "no stack allowed for MRC image. For take 2D slice out of 3D image, read the 3D image first, then use get_clip().");
        }
 
        init();
 
        check_read_access(image_index);
        check_region(area, IntSize(nx, ny));
        int xlen = 0, ylen = 0;
        EMUtil::get_region_dims(area, nx, &xlen, ny, &ylen);
 
        dict["nx"] = xlen;
        dict["ny"] = ylen;
        dict["nz"] = 1;
 
        dict["PGM.max_gray"] = maxval;
        dict["PGM.min_gray"] = minval;
 
        EXITFUNC;
        return 0;
}
 
int PgmIO::write_header(const Dict & dict, int image_index, const Region*,
                                                EMUtil::EMDataType, bool)
{
        ENTERFUNC;
        int err = 0;
 
        //single image format, index can only be zero
        if(image_index == -1) {
                image_index = 0;
        }
        if(image_index != 0) {
                throw ImageWriteException(filename, "PGM file does not support stack.");
        }
        check_write_access(rw_mode, image_index);
 
        int nz = dict["nz"];
        if ((int)nz != 1) {
                LOGERR("Cannot write 3D image as PGM. Your image nz = %d", nz);
                err = 1;
                throw ImageWriteException("N/A", "Cannot write 3D image as PGM.");
        }
        else {
                nx = dict["nx"];
                ny = dict["ny"];
 
                if (dict.has_key("min_grey")) minval = dict["min_gray"];
                if (dict.has_key("max_grey")) maxval = dict["max_gray"];
 
                // if we didn't get any good values from attributes, assign to 255 by default
 
                if (maxval <= minval || Util::is_nan(minval) || Util::is_nan(maxval)) {
                        maxval = 255;
                }
 
                EMUtil::getRenderLimits(dict, rendermin, rendermax, renderbits);
 
                fprintf(file, "%s\n%d %d\n%d\n", MAGIC_BINARY, nx, ny, maxval);
        }
 
        EXITFUNC;
        return err;
}
 
int PgmIO::read_data(float *data, int image_index, const Region * area, bool)
{
        ENTERFUNC;
 
        //single image format, index can only be zero
        image_index = 0;
        check_read_access(image_index, data);
        check_region(area, IntSize(nx, ny));
 
        portable_fseek(file, file_offset, SEEK_SET);
 
        unsigned char *cdata = (unsigned char *) (data);
        size_t mode_size = sizeof(unsigned char);
 
        EMUtil::process_region_io(cdata, file, READ_ONLY, image_index,
                                                          mode_size, nx, ny, 1, area, true);
 
        int xlen = 0, ylen = 0;
        EMUtil::get_region_dims(area, nx, &xlen, ny, &ylen);
 
        for (int k = xlen * ylen - 1; k >= 0; k--) {
                data[k] = static_cast < float >(cdata[k]);
        }
 
        EXITFUNC;
        return 0;
}
 
int PgmIO::write_data(float *data, int image_index, const Region* area,
                                          EMUtil::EMDataType, bool)
{
        ENTERFUNC;
 
        //single image format, index can only be zero
        image_index = 0;
/*      if(area && (area->size[0]!=nx || area->size[1]!=ny)) {
                throw ImageWriteException("N/A", "No region writing for PGM images");
        }
*/
 
        check_write_access(rw_mode, image_index, 1, data);
        check_region(area, IntSize(nx, ny));
 
        if (renderbits==0 || renderbits>8) renderbits=8;
 
        // If we didn't get any parameters in 'render_min' or 'render_max', we need to find some good ones
        EMUtil::getRenderMinMax(data, nx, ny, rendermin, rendermax, renderbits);
 
        unsigned char *cdata=(unsigned char *)malloc(nx*ny);    //cdata is the normalized data
 
        int old_add = 0;
        int new_add = 0;
        for( int j=0; j<ny; ++j ) {
                for( int i=0; i<nx; ++i) {
                        old_add = j*nx+i;
                        new_add = (ny-1-j)*nx + i;
                        if( data[old_add]<rendermin ) {
                                cdata[new_add] = 0;
                        }
                        else if( data[old_add]>rendermax )
                        {
                                cdata[new_add] = 255;
                        }
                        else {
                                cdata[new_add] = (unsigned char)((data[old_add]-rendermin)/(rendermax-rendermin)*256.0);
                        }
                }
        }
 
        size_t mode_size = sizeof(unsigned char);
        //fwrite(cdata, nx, ny, pgm_file);
        EMUtil::process_region_io(cdata, file, WRITE_ONLY, image_index,
                                                          mode_size, nx, ny, 1, area);
 
        free(cdata);
        EXITFUNC;
        return 0;
}
 
void PgmIO::flush()
{
        fflush(file);
}
 
 
bool PgmIO::is_complex_mode()
{
        return false;
}
 
bool PgmIO::is_image_big_endian()
{
        init();
        return is_big_endian;
}